Good guy Bad guy
by LunaGuineverePond
Summary: SORT-OF SEQUEL TO HOW HE DID IT: A WHOVIANS THEORY. First chapter concerns the reunion between John and Sherlock. If you're into Star Trek, read on for the story of a mysterious link between two men living centuries apart. They may have similar mental capacities, but their morals could not be more different. CONTAINS SPOILERS FOR STAR TREK: INTO DARKNESS.
1. Chapter 1

Sherlock stood infront of the familier numbered black door on Baker Street and ran through the events of the past few days in his head. He tried to convince himself that the reason for doing this was to double check he hadn't missed anything important, but deep down he knew it was simply because he was trying to put off what he planned to do when he walked through that door.

He had watched the two figures in the graveyard from a safe distance and, when she left, pulled Mrs Hudson behind the large gravestone that served as his hiding place. After successfully stifling that irritating scream that all women seemed to insist on producing at the most inconvenient of moments, he explained everything to her. To his surprise, she had accepted the facts fairly quickly after the initial shock. Then again, maybe it wasn't such a surprise. Under that layer of old lady-ish fluffiness was really quite a tough, tolerant woman. He smiled fondly to himself.

His smiled faded to a scowl as the memory of Lestrade's reaction surfaced.

Mycroft had insisted on going in first to explain the matter in a slightly more diplomatic way than Sherlock had planned. As Sherlock had expected, Lestrade hadn't believed a word until Sherlock got so bored of listening to it that he just walked in. This had earned a disaproving glare from Mycroft while the blood drained from Lestrade's face and he stammered and stuttered before collapsing into a chair, much to Sherlock's amusement. This amusement gave way to annoyance when Lestrade recovered and vented his feelings, telling Sherlock exactly what he thought of his 'dramatic stunt'.

After leaving Lestrade with a pot of strong coffee, the pair left and Sherlock was forced to endure another lecture from his brother about how he should stop being so dramatic about things all the time.

Now he found himself about to confront his best friend with an order to 'be sensitive'. With a sigh of resignation, he pushed the doorbell. He had barely time to remove his finger when the door was flung open and the beaming face of Mrs Hudson looked out at him.

"Well it's about time too young man, I was wondering how long it would take you to finally turn up and put poor John out of his misery. I almost did it myself, damn the consequences. If those assassins had shown up again I would have given them such a wallop with my saucepan, let me tell you. Do you know, John has really taken your apparent death badly for an ex-soldier who has watched plenty of friends and collegues meet their end. All he does is..."

And on and on, as she led him up the stairs towards the flat he had shared for so long with his friend. He tuned her out, concentrating intead on resisting the overwhelming urge to turn and run. He got the same feeling everytime he was required to do something tricky on the emotional level but this was something else. Something deeper.

Mrs Hudson knocked on the door and entered.

"Someone to see you dear."

"I don't want to see anyone," John replied from his spot by the curtains where he was staring absent mindedly out of the window.

"You'll want to see this person. I'll leave you together."

"For heaven sake woman, just tell them I-"

But his eyes widened as he turned round and was greated with the impossible site of the door being closed behind his best friend, leaving him alone in the room with what he could only assume was an apparation of some kind.

"Hello," said the apparation awkwardly.

John dropped the cup of tea he was holding. "I...you're..."

"Not dead?" Sherlock offered.

"But...how..."

"And I'm not a fake either."

"I know...you..."

But that was as far as John got before he did something he had never done in his life and would probably never do again.

He fainted.

A few minutes later, he woke up on the sofa with the memory of everything turning black and Sherlock lunging towards him. He opened his eyes to the site of Sherlock sitting in an armchair, watching him.

"How are you feeling?" Sherlock asked.

"Confused," John replied. "Explain. Now."

Sherlock took a deep breath and launched into the story of the whole Moriarty/assassin conundrum.

"That bastard," John said, sounding more like himself. "But I saw you fall. How did you survive?"

Sherlock explained about the doctor, but John just laughed at him.

"Really? You expect me to believe you had help from some guy with a magic spaceship? Look just cut the-"

As if on que, there came a funny wheezing, groaning sound and a mysterious wind blew up that whipped the curtains into a frenzy and sent papers flying around the room. John's mouth fell open as a blue box materialised in his living room. Sherlock glanced at him with a look that said "told you so" and John returned it with an expression that said "Ok ok I believe you."

Before either of them could react furthur, the door was flung open and a floppy haired man in a bow tie bounded out, brandishing a peculier metal stick that was glowing green at the tip and emitting a strange high pitched whirring sound.

"Hello! So sorry to interrupt but I suddenly remembered that ghastly incident with the wifi and thought I'd better double check this place because we can't have them getting hold of the astonishing mind that recides here, that would never do, so I just want to-"

He had been rushing around the room scanning the walls and furniture but suddenly stopped in his tracks and frowned at the mysterious instrument in his hand. He held it out and slowly turned on his heel and aimed it in turn at Sherlock and then the TARDIS.

Sherlock cleared his throat, throwing the doctor out of his reverie. He looked from Sherlock, to John, and back again. Understanding suddenly dawned on his face.

"Oh. You've told him?"

"Just now yes."

"Bad timing?"

"A little. And don't pretend you're here to check the wifi. You're checking up on us aren't you?"

The doctor sighed. "Ok you got me. I wanted to check everything was alright with you two."

He walked over to the sofa and laid a hand on John's shoulder. "You ok with all this?"

"Guess I'll have to be won't I?"

The doctor beamed at him. "Excellent! I can clearly see why he chose you as his companion."

"His-"

"Well I'd best be off! Ta ta! I just want to check..." He pointed the sonic screwdriver at Sherlock again and then at the TARDIS before examining it thoughtfully.

"Everything all right?" Sherlock enquired.

"What? Yes yes, of course, just a slight...but it's probably nothing...I'd better go, bye!"

He rushed back into the TARDIS and the pair watched as it dematerialised.

"He left rather abrubtly. What was that all about?" John asked.

"Don't know," said Sherlock. "Probably nothing important. He's a peculiar one. Tea?"

"Yes please," John said gratefully, deciding not to point out that Sherlock, a man who blew holes in the wall when he was bored, had no business calling anyone peculiar.

Little did the friends know that their lives would soon become more peculiar than ever, and they would be seeing much more of that peculiar floppy haired man in a bow tie who just landed a time machine in their living room.


	2. Chapter 2

**Ok, so I've just noticed a few spelling errors in the previous chapter. I can spell, honest! I just seem to be incapable of proof reading properly...  
Anyway, now comes the Star Trek story. Enjoy! And please leave a review it would make my day :)**

_An explosion._

Some sort of conference room full of screaming people.

A dashboard that did not exist in any modern car.

A blond boy staring at him in horror before the scene was engulfed in yellow light...

Sherlock jerked awake and sat up, heart thumping and mind racing. This was not the first dream of this nature that he'd had, but it was certainly the most vivid so far. What did it all mean?

As his breathing slowed and he began to feel calmer, he lay back and stared thoughtfully at the ceiling. He tried to recall all the dreams he'd had in the past week since his return to Baker Street.

Until this one, they'd never been very detailed. Mainly explosions and incoherent voices, along with glimpses of strange creatures and people rushing around what looked like the interior of some sort of spaceship.

There were two people that he did remember seeing a lot of, however: the blond boy that had featured in this dream and a strange looking black haired boy with pointy ears. Some sort of elf? Surely not...

None of the dreams were very pleasant, but this one in particular troubled him. It wasn't just people being killed in explosions. This time, it was him that was causing them. He was sure of it. The rockets, or whatever they were, were being fired from the spaceship that he was sitting in and it was his hands on the controls. Those people were dying because of him...

He got up, stretched, then pulled on his dressing gown and headed out of his room into the lounge where John was already dressed and sitting in his usual armchair, reading a paper and sipping tea. He looked up when Sherlock walked in.

"Another dream?" he inquired, noticing his friend's anxious expression.

Sherlock nodded wordlessly and sat down opposite his friend. John sighed, then folded his paper and put it to one side.

"Same as the others?"

"No," Sherlock replied, and told John exactly what he had seen.

"Why are you so sure it was you killing those people?" John asked. "Couldn't you have just been seeing it from the killer's point of view?"

Sherlock shook his head. "It felt too real. I could actually feel the spaceship moving and the controls under my hand. But I couldn't control myself. It was like I was in someone else's body. The body of a killer."

He got up and began to pace.

"There must be a logical explanation," he muttered. "But it's like I'm seeing another world. The spaceships, the alien creatures…it's like I'm seeing the future…"

He broke off suddenly and stopped, eyes widening in sudden realization.

"What is it?" John asked, recognising the expression of sudden enlightenment Sherlock always wore when he had just spontaneously solved a particularly tricky case.

"The future!" Sherlock said excitedly. "I'm seeing the future from the perspective of a person living there!"

"What?!" said John, exasperated. "Don't be ridiculous…"

"But it makes sense!" Sherlock cried. "If you forget how impossible it is, it makes perfect sense! All that high tech stuff…it's like something out of a science fiction film. The future…"

He shook his head, utterly bewildered.

"There are not many things that are beyond me John," he said.

John raised an eyebrow at this remark.

"But this is one of them," Sherlock continued. "There's only one person I can consult."

"The doctor?" John offered.

Sherlock smiled proudly at his friend. "Catch on quick, don't you?"

Half an hour later, Sherlock sat fully dressed in the armchair opposite John's. They waited patiently as the TARDIS materialised in their living room, after making sure all their loose papers were weighed down. It had taken them ages to tidy up after the doctor's last visit.

Sherlock had ensured that Mrs Hudson was out before calling the doctor and explaining the situation to him. She had never pressed for details on how Sherlock had survived the fall and for that he was grateful – it was hard enough trying to convince his trusting best friend of the existence of a 900-odd-year-old alien with a time machine without its timely arrival right under their noses, let alone their stubborn landlady.

Plus, he didn't like to admit that he'd needed to enlist the help of not one but three people (including Molly and the homeless person on the bike) in order to convincingly commit suicide without actually dying.

At last, the wheezing and groaning petered out and as soon as the old time machine gained a solid form, the doors where flung open and the doctor bounded out, beaming.

"Sherlock!" he cried, swooping down and kissing the bemused detective on both cheeks. "It's good to see you again so soon old pal. And you Dr Watson!" he continued, subjecting an equally bemused John to the same greeting.

Sherlock decided to overlook this embarrassing display of affection.

"I'm so grateful to you for coming," he began, but the doctor dismissed him with a wave.

"Oh it's fine," he said. "I'm grateful to you for livening things up a bit. I've just been planet hopping, which I assure you is not as exciting as it sounds when you're alone and you've seen it all before anyway. Life's been a bit boring lately, and this is just the sort of mystery that will spice up the uneventful life of an old timelord."

"I know how you feel," Sherlock said sympathetically. "Great minds like ours are particularly prone to boredom."

"I doubt any other great minds blow holes in their wall with a handgun though," John pointed out.

"It's certainly obvious how you amuse yourself," the doctor said, tutting disapprovingly at the bullet peppered smiley face embellishing the wallpaper (which John still hadn't got round to getting repaired. Sherlock, on the other hand, didn't seem too bothered).

"But enough chatter," the doctor said, clapping his hands and grinning widely once again. "We have a mystery to solve! If you wouldn't mind relaying the details once more while I give your living room the once over, that would be splendid."

Sherlock obliged as the doctor whipped out his sonic screwdriver and began scanning the room and much the same fashion as the previous week.

As Sherlock finished describing his most recent dream, he noticed that the doctor was repeatedly aiming the sonic in his direction. It was always very deliberate however – as if he was tracing a route that led repeatedly back to him.

He continued in this way after Sherlock finished, the frown on his face increasing in intensity. Eventually, John broke the silence.

"So what does in all mean?" he asked. "You're meant to be the expert. Why's he having these dreams?"

The doctor looked at him suddenly as if only just noticing him there.

"They're not dreams," he said grimly.

"What are you talking about? Of course they're dreams. What else are they going to be?"

"They seem to be unconscious post-present visions of some kind," the doctor said matter-of-factly.

"Oh please," John scoffed. "You mean he's seeing into the future? That's ridiculous! I mean, he's brilliant and everything but he's not some crazy gypsy fortune teller."

"Of course not," the doctor said. "It's not as simple as all that. Visions of that detail and vividness don't just happen. Even a mind as fine as Sherlock's would need some kind of psychic boost. And a psychic boost powerful enough to act over that amount of time can be dangerous."

"Oh come on," John began. But as he glanced in Sherlock's direction he was met with a look that said _shut up now_, which he did. Which was weird for both of then seeing as it was usually the other way round. Sherlock turned to the doctor.

"I take it from your similar behaviour in this room last week," he said "that you already have an inkling as to where this psychic boost comes from?"

The doctor's face relaxed and he smiled once more.

"Don't miss a trick do you?" he said. "Yes, I took the liberty of harvesting a trace of what I found. I assumed that it was background energy from that dodgy wifi network, which I had to admit I wasn't expecting to find. But I deactivated it and stored it in the TARDIS's Signal Storage System, just in case. And it seems it was just as well I did, because what is still residing here has become so deeply embedded it would be much trickier to extract it. It's also increased significantly in strength, and it seems to centre on you."

"So what do we do?"

"We reactivate it and trace it back to its source."

The doctor strode across the room to the TARDIS, flung open the doors and turned back to Sherlock.

"I suppose you'll want to come with me?"

"Of course," Sherlock leapt to his feet, eyes shining at the prospect of adventure and excitement. He turned to John.

"Coming?"

"I don't know…" John said, still skeptical and eyeing the TARDIS warily.

"Could be dangerous," the doctor warned. This phrase seemed to trigger something in the old soldier.

"Well why didn't you say so?" John exclaimed, jumping up and grinning like and excitable young schoolboy. "Come on, we need to get this thing out of here before Mrs Hudson gets back." And with that, he strode past the bemused forms of the two geniuses, who raised their eyebrows at each other before following him.

"It won't take me long to extract the signal and hook it up to the navigation system," the doctor said briskly, skirting around the stunned form of John Watson and heading for the central console. "But after that, I have no control over where we're going and things could get bumpy, so hold tight."

Sherlock stepped up to the console and held tightly onto the side, as did the still stunned-into-silence John, who decided to save his burning questions for later. The doctor tapped a few buttons then yanked on a lever, causing the TARDIS to wheeze and groan its way out of 221b Baker Street, taking its inhabitants with it.

The doctor usually loved the mystery of not knowing where his old ship was taking him, but his excitable grin faded into a frown and then an expression of shocked realisation as he examined the TARDIS monitor.

As the signal clearly originated from Sherlock, he was expecting it to display a picture of him and he was half right. It was the other half that worried him.

The picture was changing, switching rapidly between images of two people. One was Sherlock, the other he recognised as Khaan, the notorious villain living way in the future who left chaos and destruction in his wake. The pictures weren't side by side, which is how they would be if the two men simply shared a psychic link, which would have been bad enough. No, the images where fighting for the same space on the screen which was a lot more worrying. The doctor reluctantly and disbelievingly came to the only possible conclusion.

Khaan and Sherlock were the same person.

**Huge apologies for the insane length and distinct lack of action, I'm afraid I got a little carried away with the chatter! Please don't be put off, I promise it will get more exciting.**


	3. Chapter 3

**Sorry for the insanely long wait, I had the mother of all writers blocks…it finally shifted though **** Please leave a review, that would be most kind.**

Kirk and Spock strolled through the gleaming corridors of the main base, arguing.

"I still say we should have killed him," Kirk said stubbornly.

"As I have mentioned multiple times before, I strongly disagree," Spock countered.

"Oh do you now."

"Yes."

"Care to explain, O great and mighty Vulcan genius whose intelligence knows no bounds?"

"Certainly," Spock said, choosing to ignore the jibe at his mental capabilities. Or possibly just not recognising the sarcasm. "First off, the reviving qualities of Khan's blood could once again come in useful."

"So could the blood of any of his crew," Kirk pointed out.

"True," Spock admitted. "But seeing as his body has been active more recently, the blood would be-"

"Yes yes, whatever," Kirk said impatiently. "Skip the science lecture. Any other reasons?"

"I haven't really got any more," Spock admitted. "But think on this. He is essentially at your mercy, and if you kill him in cold blood how much difference would the two of you really be?"

Kirk opened his mouth but, when no argument sprang to mind, closed it again and muttered darkly to himself about people being too saintly for their own good. Spock allowed himself a small, triumphant smirk.

Suddenly, a door banged open behind them and a familiar, insistent cry echoed down the corridor.

"Keptin Kirk! Keptin Kirk!"

Kirk turned around, sighing, as the owner of the voice skidded to a halt beside him.

"What is it now, Chekov?" he said. "Can't a guy take a break?"

"Wisitor's sir! In ze parking lot. Come quickly!"

"What kind of visitors? If it's that blasted safety inspector again…"

"No Keptin!" Chekov was nearly jumping up and down with excitement. "Come and see!"

Before Kirk could protest, Chekov seized his arm and proceeded to drag him down the corridor.

"You too Mr Spock!" he called over his shoulder. "You'll want to see zis!"

Bemused, Spock followed his colleagues out of the building and into the parking lot. Here, several guards were pointing guns at a peculiar looking blue box and its three inhabitants who were standing outside its doors with their arms raised - one staring around in bewilderment, one watching the guards with bored indifference and one smiling warmly at the approaching trio as if they were joining a party.

"Hello there!" the doctor said, bounding forward and wringing Kirk's hand. "You must be Captain James Kirk of the USS Enterprise. I've heard so much about you. And you, Spock!" he continued, turning to Kirk's second-in-command and shaking his hand too. "I'm rather a fan of yours if you don't mind me saying so."

"Uh, thanks," Spock said. "And you are…?"

"The doctor…" Kirk whispered in awe. "You are aren't you? The last Time Lord. Everyone's heard of you."

This was of course perfectly true, and was also the reason the guards had allowed the doctor to approach their Captain so casually. It had taken them a while but now most of them were muttering to each other in excitement, weapons forgotten (although a couple of the more wary ones continued to cover the two strangers who were still hovering outside the TARDIS).

"Allow me to introduce you," the doctor said, bounding back to him friends, still beaming. Kirk and Spock followed him, Kirk nodding at the guards in a silent instruction to stand down.

"Spock, Captain Kirk, this is Dr John Watson and Sherlock Holmes."

Kirk and Spock exchanged nods with John, but then froze as their eyes fell on Sherlock. The doctor noticed.

"Ah," he muttered. "I thought we might come to this. Now it's not what it looks like," he began.

"Doctor," Kirk said weakly. "This man looks exactly like Khan."

"I know but-"

"Excuse me," Sherlock interrupted. "Would someone care to explain?"

"You look exactly like a criminal we just locked up," Kirk explained. "And I mean exactly. It's…surreal."

Sherlock nodded thoughtfully and turned to the doctor. "Could this be something to do with the psychic link?"

"Quite possibly," the doctor said hesitantly. He turned to Kirk. "I found a strange psychic link connecting Sherlock and the TARDIS. I managed to pick it up and trace it back to here."

Kirk looked confused. "The TARDIS? What's your ship got to do with Khan or this man?"

"I think I can answer that," Spock said. He'd been inspecting the time machine. "Come and look at this."

The doctor and Kirk, followed by Sherlock and John, joined him round the back of the TARDIS where he was inspecting something embedded in the woodwork.

"It appears to be a Pensive Disk," he explained.

"A what disk?" Sherlock asked.

"It's a small golden disk used to store memory's, similar to a memory stick," the doctor said, staring at the small burn mark in horror. He ran his finger over it. "That will leave a permanent mark," he said, mortified.

"Doctor," Kirk said. "Concentrate."

"Right. Yes." The doctor whipped out his sonic screwdriver and scanned the small black hole.

"Yup, it's definitely the source," he confirmed.

"Are you able to extract it?" Kirk asked.

"I can try," the doctor said doubtfully. "It could take a while though."

"I'll leave you to it then," Kirk said. "In the meantime…" he turned to Sherlock. "I'm afraid I'm going to have to place you under arrest until this is sorted out."

"What?!" Sherlock said, at the same time John said "No!" while the doctor contributed with "You can't!"

"I'm afraid I have no choice," Kirk said firmly. "Khan has caused too many problems. We'll put you in a guest room rather than a cell. You'll be perfectly comfortable."

"If you're arresting him, you'll have to take me too," John said fiercely, ignoring Sherlock's _shut up _glare.

"Very well. I really am sorry. If you need anything, please don't hesitate to ask."

Sherlock and John were led away by a group of guards while the doctor looked on hopelessly. This was not how he had pictured their first trip in the TARDIS.

"Captain," Spock said.

Kirk turned to him, sighing. "Let me guess. I did the wrong thing."

"On the contrary," Spock said. "I would have done the same. But I was going to say: why don't we just ask Khan?"

Kirk stared at him.

"Seriously? We've just arrested a guy because he's the spitting image of Khan and now you want to wake the real Khan up again? How do we know he'll even tell the truth?"

"On the balance of probability, I'm inclined to believe he will tell the truth. He has nothing to lose after all."

"Nothing to gain, either."

"True," Spock admitted. "But it's still worth a try."

Kirk turned to the doctor. "What do you think?"

"I agree," the doctor said without a thought.

"Right then," Kirk said. "Chekov, get every armed guard that isn't busy and tell them to report to me immediately. If they are busy, tell them to drop what they're doing immediately and report to me anyway. Within reason of course."

"Yes keptin." Chekov ran off.

Kirk turned to the doctor. "I guess the disk can wait. Ready to meet the biggest asshole ever?"

"Sure," the doctor replied. "It's gonna be fun."


	4. Chapter 4

Soon the doctor, Kirk and Spock were all assembled around a large glass cell. At the doctor's insistence, John and Sherlock were also there accompanied by a heavily armed escort.

From inside the cell Khan looked out at his audience with mild interest, as if they were a display of artefacts in a museum. His gaze continuously flicked back to Sherlock, and the crease between his eyebrows deepened.

"Curious," he muttered to himself. "Most curious."

"Care to elaborate?" Kirk said icily. "We know this is something to do with you."

A lopsided smirk passed fleetingly over Khan's face. "I suppose trying to convince you that this is nothing to do with me would be utterly futile?"

Kirk glared at him. Khan sighed.

"Ok," he said, sitting down. "Here's what I did."

As he talked, John found his mind glazing over what Khan was saying (a lot of which he didn't understand anyway). His mind was whirling in the way it does when you are faced with a situation that is undeniably real but still utterly impossible. And it's all the more mind-bending when that situation involves someone you are very close to. John found himself examining the dangerous criminal sitting before him. His movements were slow and deliberate, with an underlying aggression simmering beneath them. He didn't find it at all difficult to believe that this man was perfectly capable of murdering thousands of people. He was muscular, obviously used to welding heavy weapons and throwing skull shattering punches. But John's gaze was repeatedly drawn back to Khan's face. His eyes, like Sherlock's, were hard. But while Sherlock's eyes ordinarily displayed no emotion at all, Khan's screamed hate. A hate for all of humankind, a hate that may or may not have a motive behind it.

The conclusion that John drew from his analysis was – apart from the voice and facial features - this man was the complete opposite of Sherlock Holmes.

Meanwhile the doctor, Kirk and Spock listened with rapt attention.

"I noticed the Pensive disk when you first captured me and I was being assessed by one of your scientists. Charming man, a little dopey though if you don't mind me saying so. He turned his back for a minute and I seized the opportunity to swipe it from the shelf beside me, hiding it up my sleeve. I didn't for one minute think I could get away with it, but what did I have to lose? I was already a prisoner with no apparent means of escape. I took it back to my cell with me and over the next few days I made a copy of my - how shall I put it? Personality? No it's more than that. My being or conscience would be more accurate. I made a copy of my conscience and transferred it to the disc."

Kirk stared at him, aghast. "You did what?!"

"I temporarily double my conscience and implanted it into –"

"I get what you did," Kirk said impatiently. "But how? P-disks are only designed to store thoughts, not whole consciences."

"For you maybe," Khan smirked. "But not for me. I am, quite simply, better than you."

Kirk scowled at him. Spock laid a calming hand on his arm then turned back to Khan. "Please continue," he said coolly.

"The rest was easy," Khan went on. "As Kirk and I were hurtling through space, I released it. I knew it would need a power source to latch onto so that it could continue to store my consciousness. I was confident that nothing made by your puny species would suffice; only something far more advanced than any human technology would be capable of carrying out the task I had programmed into it. Possibly even..." he turned to the doctor "…timelord technology."

"The TARDIS," the doctor whispered, mortified.

"But why?" Spock asked. "What were you hoping to achieve?"

"Eventually, I know my conscience would rebuild itself into a seemingly new individual. I was prepared to wait, but eventually there would be-"

"A brand new Khan, ready to continue your reign of terror," Kirk finished.

"Yes," Khan said. He glanced at Sherlock. "It doesn't appear to have worked though, as this lookalike does not appear to be killing you all."

Sherlock met his gaze and Khan stared back, trying to work out what the deal was with this failed creation of his. But before either of them could speak, Kirk gave the order for Khan to be returned to his capsule and the doctor, Kirk, Spock, Sherlock and John headed off to inspect the TARDIS. John kept glancing at Sherlock, trying to figure out what his friend made of this devastating news about the nature of his existence. But the detective's face remained as expressionless as ever.

They reached the TARDIS and the doctor immediately focussed all his attentions on the burn mark left by the P-disk. He prodded and waved the sonic screwdriver over it, all the time muttering to himself. John, Kirk and Spock watched him more intently than was necessary – they were all avoiding looking at Sherlock.

Sherlock appreciated this – he needed time to think. His whole world had just collapsed around him. He'd always been sure of so many things, but now he didn't know how much of those things had been real…or even how much of him was real. He'd always known he'd been different, but he just assumed his brain was wired differently. Now he felt like his whole being was a lie. Any normal person would have curled up and cried at this point, but Sherlock was definitely not normal. He was more of a freak than he originally thought, but that freakiness is what kept him from collapsing onto the floor and sobbing like a three year old.

So he stood there, utterly impassive. Revealing nothing.

Suddenly, the doctor gave a cry of triumph and held up a small golden disk about the size of a 2p coin.

"Got it!" he said, beaming around at the solemn faces observing him. "Oh don't look like that," he said. "It's not as bad as you think."

"Isn't it?" John challenged.

"No," the doctor said firmly. "It was a stroke of luck that he disk hit the TARDIS and nothing else. Khan underestimated time lord technology. The TARDIS is not just a ship; she is a living, thinking being. And she thought it would not do to recreate that villain you have safely locked up, so she effectively reversed his personality," he turned to Sherlock. "And made you."

"Really?" Sherlock said softly, a glimmer of hope rising within him. That box of the doctor's was truly remarkable and to be connected to it in such a way…

"Yep," the doctor said. "Although she is an old girl so she may also have been a tad confused, but she meant well. Bless her." He smiled fondly at his ship.

"May I see the disk?" Spock asked. The doctor handed it to him.

"Remarkable," he murmured, turning it over in his hands. He looked at Sherlock. "You do realise that this thing contains your entire existence?"

Sherlock just stared at it wordlessly. Kirk was watching him suspiciously. He wasn't sure if he trusted him or not. How did he know that Sherlock's very presence didn't put them all at risk? If there was even the slightest possibility that he could turn at any moment…

There was only one thing he could do.

"Let me see it," he said, holding out his hand. Spock handed it over, momentarily forgetting how dangerously impulsive Kirk could be.

Kirk studied it for a moment. Then he dropped it to the ground and stomped on it, grinding it into pieces.

The doctor, John and Spock gave spontaneous cries of protest, while Sherlock suddenly had the sense of something slamming into his gut, hard.

He then, quite literally, began to slowly fade from existence.


	5. Chapter 5

Several thousand years in the past and across the ocean in modern day London, Mycroft sat stirring a cup of tea. He was also debating whether or not to drop Sherlock a text. A week was normally an acceptable amount of time to wait before checking up on an irresponsible younger brother, but Sherlock was not your everyday irresponsible younger brother. He would probably accuse Mycroft of fussing like an old woman but still…sending a text would put his mind at rest a little even if he didn't get a reply. Also his tea was still far too hot to drink. Now, where did he leave his phone? Ah, there it was on the windowsill. He got up, walked round his desk and picked it up. It took a while to switch on and it occurred to him that it might be quicker to make use of the silent mode more often. He flicked through his contacts. Who was he going to text again? Oh yes. Lestrade. Must see how he's getting on with his latest murder case…

Molly pottered around the lab, tidying, organising and generally making it look a little more presentable. At least, that's what she made herself believe – in reality, she was just passing the last 15 minutes of the day before she could go home. When 5 o' clock finally arrived, she surveyed her work with a satisfied air. The lab looked much tidier, and checking the incubators for any stray e-coli colonies had left her feeling a little more relaxed. After all, you can never trust microbiologists – they usually meant well, but were often a little careless about where they leave potentially pathogenic bacteria. There was just one other thing bothering her. An old riding crop was leaning against the wall in the corner of the lab. Her first thought had been to throw it away, or at least hand it into lost property – although she had no clue as to who it could belong to. But something was nagging her at the back of her mind…maybe she should leave it where it was…just in case someone came looking for it.

Mrs Hudson wandered down the supermarket isle, checking her shopping list. Eggs, milk, bread, cigarettes…hang on. She didn't smoke and neither did John. Why did she have cigarettes written down? She crossed them out, silently cursing old age and the deteriorating mind that was bound to come with it sooner or later.

Meanwhile, Lestrade sat at his desk, puzzling over his most recent case and wishing there was someone he could consult…

John grabbed at his friend but his hand passed right through Sherlock as if he was a ghost.

"Sherlock!"

"Alright, everybody stay calm!" the doctor said, sounding decidedly un-calm.

"Sherlock!" John yelled again, sounding downright hysterical.

The doctor ran circles around the slowly depleting form of Sherlock, muttering frantically about time streams and maintaining signals.

"Sher- AAARGH!" John sank to his knees, clutching his head. The doctor rushed to his side.

"John? What is it?"

"My head…pictures …"

He groaned as a fresh wave of nausea stole over him and images stabbed at his brain. Sherlock in a lab on their first meeting…in a taxi…wielding a gun…

"But John this is brilliant!" the doctor said excitedly. "Your mind is resisting. Listen to me; you must hang onto these images. You must remember them!"

"But it hurts," John moaned. Sherlock atop a building…leaning forward…a gravestone bearing his name… "No! Please…I need you… I don't want to be alone again…"

"Look, if we can get you to the TARDIS I-" the doctor's eyes widened as he remembered the psychic link connecting the time machine and the consulting detective.

_Sherlock observed all this with mild interest. The voices where muffled, movements sporadic. He was overwhelmed by a sense of peace. He felt as if he was floating. He closed his eyes and images flickered behind his lids. Fleeting pictures of Mrs Hudson, Lestrade, Mycroft and Molly. And then clear as crystal, John, his face lined with grief._

"I don't want to be alone."

"You won't be," Sherlock whispered.

Using the entirety of his outstanding brain power, he tugged his being back towards existence just as the doctor dashed into the TARDIS.

Kirk and Spock watched in astonishment as the TARDIS dematerialised and immediately rematerialised around the now unconscious form of John Watson curled at the nearly transparent feet of Sherlock Holmes.

In the TARDIS, the doctor relaxed a little now that Sherlock appeared to be stable. Still translucent, but stable. He had one last trick up his sleeve that might just work.

Using the number stored in John's phone and the TARDIS communication system, he hacked into Sherlock's mobile and sent four texts.

Mycroft's phone beeped in his hand, indicating a new message. It was Sherlock. 'John fine, please don't fret you'll get frown lines –SH'. Mycroft smiled to himself and, not for the first time, wondered if his brother was psychic.

Molly was just getting into her car when she received a text. Her heart leapt when she saw the sender. 'Coming in tomorrow, don't touch the riding crop I'll need it –SH'. She put her phone away and pulled out of the car park. As far as she was concerned, tomorrow couldn't come fast enough.

Mrs Hudson tried to remember back to John's lessons about using a mobile. She didn't like these new-fangled gadgets, but they were useful. After pressing a few buttons experimentally, she managed to get the text open. 'Don't forget the cigarettes –SH'.

Lestrade's phone vibrated next to his head. He jerked awake and sat up at his desk, papers stuck to his face. He picked up his phone. 'I assume you haven't found the murder weapon yet. You might want to check under the stairs –SH'.

Back in the TARDIS, Sherlock and John were engulfed by a bright white light and they both vanished.

The light cleared and John and Sherlock found themselves sitting in their armchairs in 221B Baker Street and staring at each other in bewilderment. Before either of them could say anything, a familiar wheezing and groaning filled the room and the TARDIS materialised. The doors opened and the doctor stepped, looking at them both sheepishly. There was a pause.

"Well," the doctor said awkwardly. "That turned out all right, didn't it? As well as could be expected anyway," he added quickly when John started to frown at him. "And I channelled the excess energy into sending you back here, in case you were wondering how it happened. Well, it's a little more complicated than that, but it worked and that's the main thing."

"I take it I'm not allowed to pop out of existence after all?" Sherlock said casually.

"Nope, not this time!" the doctor said cheerfully. "Although it's always good to be sure…"

He whipped out the sonic screwdriver and waved it over Sherlock.

"Yep, all clean," he said. "You're completely yourself. Well, you always were. It's just when you came into contact with the TARDIS that things got messed up a bit. The poor girl got a bit confused you see. Wasn't sure what to make of you."

"What about Kirk and Spock?" John asked. "Are they all right?"

"Oh yes, they're fine. Arguing like the most aggressive married couple in existence, but absolutely fine." He sighed. "I should probably sort them out before they kill each other." He smiled to himself. "Won't be the first time I've had to mend a marriage."

"Good luck with that," John said.

"Thanks. Well, goodbye."

"Goodbye," Sherlock said. "And thank you."

"Feel free to visit," John added.

The doctor beamed at him. "I will! Cheerio!" He re-entered the TARDIS and, with a wheeze and a groan, he was gone.

Sherlock and John sat in silence for a while, saying nothing but, at the same time, everything. Eventually, John got up and headed for the kitchen. "Tea?" he asked.

"Please."

As John pottered around the kitchen, Sherlock's phone rang. It was Mycroft.

"Sherlock? You have a call to make. Lestrade needs your help."

**Thank you so much for reading, please leave a review - all constructive criticism welcome :) PM me if you have any requests on any fandoms, I'm kinda stumped for ideas now… :/**


	6. Author's note

**Added some stuff to chapter 5, it should be up by now.**


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